The small intestinal microbiota has a crucial role in gastrointestinal health, affecting digestion, immune function, bile acid homeostasis and nutrient metabolism. The challenges of accessibility at this site mean that our knowledge of the small intestinal microbiota is less developed than of the colonic or faecal microbiota. Here, we summarize the features and fluctuations of the microbiota along the small intestinal tract, focusing on humans, and discuss physicochemical factors and assessment methods, including the technical challenges of investigating the low microbial biomass of the proximal small bowel. We highlight the essential protective mechanisms of the small intestine, including motility, the paracellular barrier and mucus, and secretory immunity, to show their roles in limiting excessive exposure of host tissues to microbial metabolites. We address current knowledge gaps, particularly the variability among individuals, the effects of dysbiosis of the small intestinal microbiota on health and how different taxa in small intestinal microbiota could compensate for each other functionally.

小肠微生物群在胃肠道健康中起着至关重要的作用，影响消化、免疫功能、胆汁酸稳态和营养代谢。该站点的可访问性挑战意味着我们对小肠微生物群的了解不如结肠或粪便微生物群发达。在这里，我们总结了小肠沿小肠微生物群的特征和波动，重点关注人类，并讨论了理化因素和评估方法，包括研究近端小肠低微生物生物量的技术挑战。我们强调了小肠的基本保护机制，包括运动、细胞旁屏障和粘液以及分泌免疫，以表明它们在限制宿主组织过度暴露于微生物代谢物中的作用。我们解决了当前的知识差距，特别是个体之间的差异、小肠微生物群失调对健康的影响以及小肠微生物群中的不同分类群如何在功能上相互补偿。